Table 2.

Chimeric transcripts found in the ENCODE regions

ENCODE region	Chromosome	Gene 1 (upstream 5′)	Transcripts 1	Promoter activity	Gene 2 (downstream 3′)	Transcripts 2	Promoter activity	Supporting EST	RT-PCR
ENm009	chr11	TRIM6	NM_001003818	45.88*	TRIM34	NM_021616	242.41*	AB039903
			NM_058166	(1.11 ± 1.57)		NM_130389	(1.06 ± 1.36)
				HTC116			MG63
ENr233	chr15	SERF2	NM_005770	929.73*	HYpk	NM_016400	1.88	AK000438
				(1.05 ± 1.66)			(1.04 ± 1.45)
				Be2C			Panc1
ENm005	chr21	CRYZL1	BC033023	82.11*	DONSON	NM_017613	9.90*	AL157441
				(1.19 ± 2.23)		NM_145794	(1.19 ± 2.23)
				JEG3		NM_145795	JEG3
ENr223	chr6	C6orf148	NM_030568	230.36*	AC019205.8-001	AK090984	115.18*	BM544101
			bA257K9.4-002	(1.05 ± 1.66)			(1.02 ± 1.12)
			bA257K9.4-001	Be2C			HMCB
ENm013	chr7	AC003076.1-001	AC003076.1-001	N/A	PFTK1	NM_012395	2.43	AF119833	Brain
							(1.22 ± 2.43)		Liver
							HepG2		Colon
									Muscle
									Testis
ENr331	chr2	Q96IW3	BC007201	2.95	Q9H8B3	AK023854	11.61*	BI559709	Muscle
				(1.09 ± 1.41)			(1.19 ± 2.23)	BG912151
				G402			JEG3
ENm005	chr21	C21orf59	NM_021254	463.68*	TCP10L	NM_144659	1.27		Heart
			NM_017835	(1.01 ± 0.74)			(1.01 ± 0.74)
			AK094456	U87			U87
			AK055328

Tandem chimeric transcripts in the ENCODE regions supported either by ESTs or RT-PCR of computational predictions, or both. Gene and Transcript identify the genes and transcripts involved in the TICs. Supporting ESTs are the ESTs supporting the TICs after our filtering protocol (see Methods). RT-PCR lists the tissues in which expression of the chimeric transcript has been detected in the RT-PCR experiment (see Fig. 2). Experimental validation of putative promoters by reporter assay is shown on the promoter activity column. The transcription start sites were predicted by assigning the 5′ end of each gene model as the transcription start site supported by full-length cDNAs. Relative reporter activity was determined by comparing the firefly luciferase/Renilla luciferase ratios of reporter constructs in 16 different cell lines (see Trinklein et al. 2003, 2004). The highest firefly luciferase/Renilla luciferase ratios values are shown together with the mean and the standard deviation of the negative controls for the corresponding cell line. Promoter fragments with a significant reporter activity (exceeding three times the standard deviation of all control fragments) are marked with an asterisk. The firefly luciferase/Renilla luciferase ratios from the promoter regions and the negative controls were obtained from the UCSC Browser.